Time-of-flight mass spectrometers, which have been known for more than 50 years, have undergone rapid development over about the last 10 years. On the one hand, these devices can advantageously be used for new types of ionization, with which large biomolecules can be ionized, and on the other hand, the development of rapid electronics for digitizing the rapidly varying ion current in the detector has made it possible to construct high resolution devices. Nowadays analog-to-digital converters with an 8 bit dynamic range and a data conversion rate of up to four gigahertz can be obtained, while for the measurement of individual ions, time-to-digital-value converters, with time resolutions in the picosecond range, exist.
Time-of-flight mass spectrometers are often referred to with the abbreviation TOF or TOF-MS.
If mass spectrometry is to be used to measure the masses of large molecules, such as occur particularly in biochemistry, the restricted mass range of other mass spectrometers means that the time-of-flight mass spectrometer is more suitable than any other spectrometer type.
Two different types of time-of-flight mass spectrometer have developed. The first type comprises time-of-flight mass spectrometers for the measurement of ions generated in pulses, for example by matrix assisted laser desorption, abbreviated to MALDI, a method of ionization appropriate for the ionization of large molecules.
The second type comprises time-of-flight mass spectrometers for the continuous injection of a beam of ions, a segment of which is ejected in a “pulser” transverse to the injection direction, and which is allowed to fly through the mass spectrometer as a linearly extended bundle of ions. This generates a ribbon-shaped ion beam. This second type is referred to for short as an orthogonal time-of-flight mass spectrometer (OTOF); it is mainly applied in association with electrospray ionization (ESI). Through the application of a very large number of pulses in a given time (up to 50,000 pulses per second) a large number of spectra, each based on a small number of ions, is generated in order to exploit the ions in the continuous ion beam most effectively. Electrospraying is also suitable for the ionization of large molecules.
These orthogonal time-of-flight mass spectrometers offer the following advantages over other mass spectrometers used for continuous ion beams:                (1) They have a very wide range of masses, even though this is restricted again by a very high pulse rate. At pulse rates of 20 kilohertz, however, it is still possible to achieve a mass range of about 5000 atomic mass units.        (2) They can follow a very rapidly changing substance supply, such as may emerge from a high resolution chromatographic or electrophoretic separator, with great speed, for instance by delivering a sum spectrum every twentieth of a second, each formed by adding a thousand individual spectra. They can, for instance, be used for electrophoretic separation of substances on a chip, which until now has not been possible with any other mass spectrometer.        (3) Above all, these mass spectrometers, even though physically relatively small, are suitable for generating outstanding precision in the mass determination. This point is of particular significance for modern molecular biochemistry and its application fields, but calls for considerable efforts to be made to condition the ion beam injected into the pulser, and for the development of a good pulser that supplies very well resolved ion signals with a highly reproducible, ideally symmetrical, form.        
The pulser is always operated in two, repeatedly alternating, phases: (1) the filling phase, in which a fine beam of ions with a diameter of only about one millimeter, consisting of ions moving as parallel as possible, enters into the pulser region and crosses it until the pulser region is just filled with ions having the desired range of masses, and (2) the acceleration phase in which the flying ions are ejected transversely as a pulse and accelerated into the mass spectrometer's drift region. The potentials must be switched over at the start of the acceleration phase extremely fast, within a few tens of nanoseconds. The original flight direction of the low energy ions in the fine ion beam is referred to as the x-direction, and the ions are then pulsed out with high energy, perpendicularly, in the y-direction. The resulting flight direction depends on the relationship of the kinetic energies in the x and y directions; it is close to the y-direction, but is not entirely identical with it.
In principle, the pulser has a very simple construction; the pulser region into which the parallel ion stream is injected in the x-direction is located between a pusher or repeller diaphragm and a puller diaphragm. The pusher does not usually have any apertures. The puller either has a grid or a fine slit through which the ions are ejected as a pulse in the y-direction. The pusher and puller here only carry a small proportion of the entire acceleration voltage, because high voltages cannot be switched with the necessary speed. A compensation diaphragm is positioned after the puller and this suppresses penetration of the main acceleration field into the pulser region. Between the puller and the field-free drift region of the mass spectrometer, at least one additional diaphragm generates the main acceleration field, which provides the major proportion of the acceleration of the ions up to the drift region. The potential is held static on the diaphragms for the main acceleration field. The drift region usually has no field.
In order to achieve high resolution, the mass spectrometer is usually fitted with an energy-focusing reflector. This reflects the ion beam that has been pulsed out towards the ion detector, and provides an accurate time focus at the detector for ions of the same mass but with slightly different energies.
For a high resolution, it is particularly important to provide compensation for the spatial spread of the ions in the y-direction within the ion beam that is injected into the pulser, because the ions from different positions within the cross section of the ion beam must travel flight paths of different lengths to reach the detector.
This spatial expansion of the ion beam within the pulser region, or in other words the finite cross-section of the ion beam consisting of ions moving in parallel, can be compensated for by focusing the distribution of the start locations of the ions according to Wiley and McLaren, (Time-of-Flight Mass Spectrometer with Improved Resolution, Rev. Scient. Instr. 26, 1150, 1955) through the distribution of the potentials across the start locations when acceleration begins. The ions with different start locations in the y-direction then start from different potentials, and therefore have slightly different kinetic energies when they have passed through all the acceleration fields. Those ions which, because of their start location, must travel a longer flight path before they reach the ion detector are given a somewhat higher energy, and therefore a higher velocity, which allows them to catch up again with those ions with a shorter flight path at a “start location focal point”. All those ions of one mass but with different start locations arrive at this start location focus at exactly the same time but with slightly different velocities.
This start location focal point is advantageously located between the pulser and the reflector. Ions of one mass arrive at this point at the same time, but they do have slightly different kinetic energies (and therefore different flight speeds). This point can therefore be thought of as a virtual ion source, from which ions of one mass start at the same time, but with differing initial velocities. These ions can now be focused by the energy-focusing reflector onto the detector in such a way that ions of one mass arrive here at precisely the same time.
A spread in the initial velocities in the pulser can also be compensated for, as already described by Wiley and McLaren, but only if there is a strict linear correlation between the start location (in the x-direction) and the initial velocity (also in the x-direction). This is, for instance, the case if the ions enter the pulser from one location with slight divergence. A spread in the initial velocities that is not correlated with the start locations cannot be compensated for, and results in a deterioration in the mass resolution capacity. This is what creates the demand for good beam conditioning if good mass resolution is to be achieved.
In commercially manufactured devices, the interior of the pulser is always separated from the electrical field of the main acceleration region by a grid. This means that the ions are pulsed out through the grid. Penetration of the main acceleration field through the grid during the filling phase is relatively slight, and can be controlled.
Grids, however, have disadvantages that are not confined to their restricted transmission and to the small angular spread of the ions caused by distortions of the potential within the grid mesh. It is, in particular, possible for scattered ions to be generated through multiple glancing contacts with the grid wires, or even through surface-induced ion fragmentation (SID=surface induced decomposition).
Pulsers having slit diaphragms are, however, also described in the literature. The most recent state of the art here was reported by A. A. Makarov in WO 01/11660 A1 (PCT/AU00/00922).
Although they have advantages, slits also create problems: the relatively strong, continuously present main acceleration field penetrates into the pulser region during the filling phase and interferes with the filling. The beam of low energy ions is diverted by the penetrating field, no longer runs along the axis of the pulser region, and can even leave the pulser region. This slit diaphragm, moreover, has a very strong focusing or defocusing effect in the acceleration phase in the z-direction (defined as being perpendicular to the x and y directions) on the ions to be accelerated, if even minor field penetration occurs during the acceleration process, i.e. if the acceleration field is not precisely the same on both sides of the puller diaphragm, so that curved equipotential surfaces are generated in the region of the slit.
A. Makarov's patent application is aimed at overcoming these two disadvantages, namely (a) penetration of the main acceleration field and (b) defocusing during the acceleration phase. Between the pulser's drawing diaphragm and the slit diaphragms for generation of the main acceleration field, Makarov inserts a slit diaphragm, referred to here as the compensation diaphragm. During the filling phase its potential relative to the puller diaphragm is selected in such a way that penetration of the main acceleration field through the compensation diaphragm and the puller diaphragm is, evidently, precisely compensated at the location of the fine ion beam (Makarov speaks of stopping the ion beam from “bleeding” out of the pulser region). In the acceleration phase, undesirable focusing effects from the puller diaphragm in the z-direction are cancelled by making the field strengths in the pulser region and in the intermediate space between the puller diaphragm and the compensation diaphragm have very much the same magnitude. There is thus hardly any field penetration during the acceleration phase; this means that curved equipotential surfaces that could create undesired focusing or defocusing are not created. As they pass through the puller diaphragm, the ions still have relatively low energy, and react strongly to curved equipotential surfaces in this region.
In detail, Makarov creates a distance between the puller diaphragm and the compensation diaphragm of exactly the same size as the distance between the pusher electrode and the puller diaphragm. Makarov here switches two potentials, that of the pusher electrode and that of the compensation diaphragm. He leaves the potential of the puller diaphragm unchanged.
During the filling phase, Makarov switches the pusher diaphragm to equal the always constant potential of the puller diaphragm, and the potential of the compensation diaphragm to a potential that generates an ion-retarding field in the pulser region, which may be referred to as compensation of the penetration. In the acceleration phase, Makarov claims to switch the potential of the pusher electrode to such a high ion-repelling potential that it compensates for an initial distribution of the ions at the detector. He claims to switch the compensation electrode to a potential that does not generate any spreading of the beam in the spectrometer's drift region transverse to the slits. He therefore sets up an almost homogenous acceleration through the various acceleration diaphragms, and makes use of only one of the diaphragms to create a slight improvement in the z-focusing (the direction transverse to the slits). It is clear to the specialist, in any case, that with this arrangement the cross section of the ion beam is optimally transferred into the drift region through a nearly homogenous acceleration field extending from the pusher electrode through to the field-free drift region without diverging.
More precise analysis, however, shows that the arrangement and operation of the pulser according to Makarov does not provide the best mass resolution of the ion beam.
The effect of keeping the puller diaphragm at a constant potential according to Makarov is that during the switching the potential in the axis of the injected ion beam is raised. However, the ion beam is injected by an ion-optical system whose last aperture diaphragm is at the potential of the ion beam. The potential of this aperture diaphragm, which is not switched, penetrates asymmetrically into the potential in the pulser region, and inevitably distorts it. It is therefore necessary to select a very long pulser region having a long inlet before the start of the slit opening in the puller diaphragm, in order to cancel out this effect. The same applies to the end of the pulser region. Operation in which the potential in the axis of the injected ion beam is not kept constant thus requires a very long pulser region, much longer than the slit length for pulsed ejection of the ion beam. For a number of reasons, however, a long pulser necessarily lowers the level to which the continuous ion beam from the ion source can be exploited.
However, even with a long pulser, i.e. in the absence of the disturbing influence of the front aperture diaphragms on the resolution, Makarov's implementation does not achieve a very high mass resolution. The reason for this appears to be that the slits in diaphragms of finite thickness still distort the field, even if the field on both sides is the same. It is not practically possible to manufacture slit diaphragms thinner than about 0.3 mm because the diaphragms must have a very high degree of flatness. With a slit width of about a millimeter, the fields penetrating into the slit from the two sides create a lens effect, even if the fields on both sides are equally strong. It is not, however, the slight lens effect that interferes with the resolution. Simulations demonstrate that the marginal beams passing through the slit close to its edges have a dramatically different passage time from the ions that pass centrally through the slit. The difference in passage time amounts to a few nanoseconds, where an attempt is being made to achieve signal widths for the mass peaks of only about two to three nanoseconds. (The desired mass precision of a few parts per million requires the signal time to be measured to within a few picoseconds accuracy.)